A 42-year-old female with gradual-onset dyspnea on exertion and a systolic murmur is presented, in whom electrocardiogram showed left axis deviation with an Rsr' pattern in lead V1. Chest X-ray had a pulmonary vascular shunt and echocardiography marked a large ostium primum atrial septal defect together with a cleft in the mitral valve, leading to a diagnosis of the partial atrioventricular septal defect. Furthermore, magnetic resonance imaging depicted an incidental cyst on the roof of the left atrium. The operation was performed, and the cyst was excised. It measured 15 mm in diameter, had a fibrotic wall and contained homogeneous gelatinous material. Histopathology showed a small simple cyst with a fibrotic wall, lined by cuboidal to respiratory-type columnar cells. No evidence of malignancy was noted. The patient had an uneventful postoperative course and was discharged in good clinical condition.